Overview

This course is for doctoral students in computer science. The main component of the course is a series of lectures and hands-on sessions. Additionally, doctoral students who are taking the course will have to work on lab assignments, and on a small project or a term paper.

The course will be delivered by experienced teachers who are part of the Semantic Web research group of the Department of Computer and Information Science (IDA) at Linköping University.

Goals

After attending the course you should:

• Be able to understand and explain the basic ideas of Knowledge Graphs and Semantic Web Technologies, including Linked Data and ontologies, and its related standards (RDF, OWL, SPARQL, ...)
• Be able to understand, retrieve, load in a triple store, query (online or offline) and use existing RDF-based Knowledge Graphs from the Web
• Be able to use an ontology engineering methodology and ontology engineering tools to design and formalize a high-quality OWL ontology, based on a specific usage scenario (set of requirements)
• Be able to evaluate, align, and repair an OWL ontology, using current methods and tools for ontology alignment, evaluation, and repair
• Be able to understand and to explain how ontologies are typically used in applications
• Have a basic idea of the current research topics and open research problems in the field

Schedule for the Lectures and Hands-On Sessions

We will meet in the room called Charles Babbage. The schedule for the course is as follows (note that some things might change slightly as we go along):

• March 2
  09:00-09:15 Course Introduction (Eva & Olaf) (slides)
  09:15-10:00 Motivation of Knowledge Graphs and the Semantic Web Vision (Olaf) (slides)
  10:00-10:45 Introduction to Ontologies (Eva) (slides)
    15 mins break
  11:00-12:00 Introduction to RDF (Olaf) (slides)
    lunch break
  13:00-13:30 Hands-on: RDF (Olaf)
  13:30-14:00 Triple Stores and SPARQL Endpoints (Olaf) (slides)
    30 mins break
  14:30-16:00 Introduction to the RDF query language SPARQL (Olaf) (slides)
  16:00-17:00 Hands-on: SPARQL (Olaf)
• March 3
  09:00-12:00 Introduction to Description Logics (Patrick) (slides)
    lunch break
  13:00-14:00 Introduction to Description Logics, cont'd (Patrick)
    15 mins break
  14:00-15:15 Publishing and Querying RDF-based Knowledge Graphs on the Web (Olaf)
• March 14
  13:00-14:30 Basic OWL modeling, incl. Protege demo (Eva) (slides)
  14:30-15:30 Hands-on: Basic OWL modeling using a tool (Eva)
    15 mins break
  15:45-16:30 Modeling methodology and requirements management (Eva) (slides)
  16:30-17:00 Hands-on: creating requirements (Eva)
• March 15
  09:00-10:30 Hands-on: creating an ontology from given requirements (Eva)
    30 mins break
  11:00-11:30 Ontology design patterns (ODPs) and ODP-based modeling methodology (Eva) (slides)
  11:30-12:00 Hands-on: Small ODP exercise (Eva)
    lunch break
  13:00-13:30 Introduction to the group project
  13:30-17:00 Hands-on: collaborative ontology engineering project
• March 16
  10:00-12:00 Ontology Alignment and Debugging (Patrick) (slides)
    lunch break
  13:00-14:00 Ontology Alignment and Debugging, cont'd (Patrick)
  14:00-15:00 Hands-on: Ontology Alignment and Debugging (Ying)
• March 21
  09:00-09:30 Ontology Visualization and Exploring RDF Knowledge Graphs (Olaf) (slides)
  09:30-10:00 Mappings-based Knowledge Graph Construction (Olaf) (slides)
  10:00-10:30 Machine Learning-based Knowledge Graph Construction (Riley) (slides)
    15 mins break
  10:45-11:45 Introduction to constraints in RDF (SHACL) (Sebastian) (slides)
  11:45-12:00 Hands-on: SHACL (Sebastian)
    lunch break
  13:00-13:45 Hands-on: SHACL, cont'd (Sebastian)
  13:45-14:15 Property Graphs (Olaf)
  14:15-14:45 Hands-on: Property Graphs (Olaf)
  14:45-15:15 RDF-star and SPARQL-star (Olaf)
    15 mins break
  15:30-16:30 Discussion of project ideas
  16:30-17:00 Wrap-up (revisit learning outcomes, etc.)

Instructions and Requirements for PhD Students

In order to receive credits/certificates for attending the course you need to do three things: 1) Actively participate in all the lectures and hands-on sessions of the course, 2) complete a set of assignments (listed below), and 3) select and complete a small project to be described in the afternoon of Macrh 21 and then done after the course week (optional, but needed to receive the full 6 credits of the course).

Assignments to be completed are (no hard deadline, but preferably complete and submit within one week from hands-on date):

• ... (will be compelted within the next few days, now only contains the ontology part)
• Complete and hand in the solution to Hands-on: basic OWL modeling using a tool, send result via e-mail to Eva
• Complete and hand in the solution to Hands-on: creating an ontology from given requirements, send result via e-mail to Eva
• Complete and hand in the solution to at least modules from Hands-on: collaborative group project, and one module that integrates at least 2 other modules (one shoudl not be your own), send result via e-mail to Eva. Stories and module to integrate with can be requested from Eva by e-mail.

For the project after the course, please think about a suitable project during the first few days of the course (if you need feedback, please discuss with the teachers), and sign up with your project idea here. In the signup form you need to provide a few sentences describing your idea/plan for the project. You can select between these two main categories of projects:

• Reading projects: select a topic from the course, read at least 5 research articles in that area, write a summary of those articles (5-10 pages)
• Practical project: select a technology discussed in the course, apply it on something related to your own PhD project, write a summary of what you did and your experience/evaluation of the technology (5-10 pages) - alternatively: a practical project provided by us

For the project you will be assigned one of the teachers as your point of contact, and although there is no hard deadline you should agree on a submission date, preferably within the next month, with your assigned teacher.

Suggestions for further reading

Books on the course topics in general (including RDF and SPARQL):

• Hogan: The Web of Data. Springer 2020.
• Hogan, Blomqvist, Cochez, et al.: Knowledge Graphs. Synthesis Lectures on Data, Semantics and Knowledge, 1-257. Morgan & Claypool. Free online version.
• Allemang, Hendler & Gandon: Semantic Web for the Working Ontologist (3rd edition)

Further reading on ontology engineering:

• Ontology tutorial for Protege (older version), using the Pizza ontology as an example.
• Allemang, Hendler & Gandon: Semantic Web for the Working Ontologist (3rd edition)
• Keet: An Introduction to Ontology Engineering
• Hitzler, P., Gangemi, A., Janowicz, K., Krisnadhi, A.A., Presutti, V.: Ontology Engineering with Ontology Design Patterns: Foundations and Applications (Contains for instance a chapter describing the XD methodology)
• Videos from a slightly outdated (10 year old) conference tutorial on the basics of the semantic Web. Many basic concepts still apply, but note that new versions of the standards (e.g. OWL2) has appeared since.
• Lambrix, Completing and Debugging Ontologies: state of the art and challenges
• Some papers on specific topics discussed, or requested by students:
  • Blomqvist, E., Hammar, K., and Presutti, V.: Engineering Ontologies with Patterns - The eXtreme Design Methodology. In: Ontology Engineering with Ontology Design Pattern - Foundations and Applications, IOS Press, 2016.
  • Dudas, M., Lohmann, S., Svatek, V., & Pavlov, D. (2018). Ontology visualization methods and tools: A survey of the state of the art. The Knowledge Engineering Review, 33, E10. doi:10.1017/S0269888918000073
  • This chapters contains quite a few examples of ontologies, and tries to describe different kinds of ontologies based on various dimensions: Roussey C., Pinet F., Kang M.A., Corcho O. (2011) An Introduction to Ontologies and Ontology Engineering. In: Ontologies in Urban Development Projects. Advanced Information and Knowledge Processing, vol 1. Springer, London. https://doi.org/10.1007/978-0-85729-724-2_2
  • Old paper discussing types of ontologies, including the image comparing types of ontologies of different levels of abstraction (c.f. Figure 4). N. Guarino: Formal ontology and information systems. In: N. Guarino (ed.), Formal Ontology in Information Systems. Proceedings of FOIS’98, Trento, Italy, 6-8 June 1998. Amsterdam, IOS Press, pp. 3-15. Extended version of the original paper can be found here.

Further reading on DL:

• Baader, Calvanese, McGuinness, Nardi, Patel-Schneider. The Description Logic Handbook. Cambridge University Press, 2003.
• Donini, Lenzerini, Nardi, Schaerf, Reasoning in description logics. Principles of knowledge representation. CSLI publications. pp 191-236. 1996.
• dl.kr.org

Further reading on SHACL and related topics:

• The W3C SHACL recommendation
• Labra Gayo, Prud'hommeaux, Boneva, Kontokostas: Validating RDF Data. Synthesis Lectures on the Semantic Web: Theory and Technology, 7:1, 1-328. Morgan & Claypool. Free online version.

Instructors and Assistants

The course will be organized by the Semantic Web research group of the Department of Computer and Information Science (IDA) at Linköping University. In particular, the course will be delivered by the following experienced teachers of the group who have in-depth expertise in the various topics covered by the course:

• Olaf Hartig is a Senior Associate Professor in Computer Science. He has a broad knowledge on topics related to the management of data and databases. His specific areas of expertise in this context focus on data on the Semantic Web and on graph data, as well as on problems of federated data management in which data is distributed over multiple, autonomous and/or heterogeneous data sources. Regarding these topics, Olaf's interests range from systems-building related research all the way to theoretical foundations. Olaf presented several tutorials at top international conferences in the Semantic Web area including WWW (2010, 2013, 2017) and ISWC (2008, 2009, 2017, 2019). At LiU, he is responsible for the Database Technology courses.
• Eva Blomqvist is a Senior Researcher. She has mainly worked on research problems related to ontologies an ontology engineering, and was one of the researchers who initially proposed the notion of ontology design patterns, about 12 years ago. During her PhD she worked on semi-automatic ontology development, so-called ontology learning. Eva has also been actively involved in the development, refinement and evaluation of the eXtreme Design ontology engineering methodology, which was the first agile ontology engineering methodology when it was proposed in 2009. More recently Eva has been involved in several projects applying ontologies in various contexts, e.g. in decision support systems, and also using ontologies and other Semantic Web technologies to perform semantic complex event processing to make sense of streaming data.
• Patrick Lambrix is a Professor and he leads the Database and Web Information Systems Group at IDA. Patrick has over 20 years of experience in research related to knowledge engineering, which includes aspects of Semantic Web, ontologies, and databases. Recent highlights include pioneering work in ontology alignment and ontology completion and debugging resulting in unique and award-winning systems. The systems and techniques developed by his group have been and are being used in different domains such as life sciences, animal health surveillance, libraries and materials design.
• Sebastian Ferrada is a Postdoctoral Researcher. His current research is focused on heterogeneous data integration for graph databases. He received his PhD from Universidad de Chile in 2021, with his thesis "Similarity-based Web Queries". His research interests also include the Semantic Web, Multimedia Databases and Information Retrieval.
• Riley Capshaw is a PhD student at the Knowledge Modeling and Cognitive Systems group at IDA. His research interests focus on the application of Natural Language Processing techniques for Ontology and Knowledge Graph generation from unstructured text documents in both automatic and guided settings.
• Daniel de Leng is a research engineer and deputy lab leader at the Reasoning and Learning lab. His research interests revolve around AI and autonomous systems. During his PhD he investigated different ways to robustly monitor safe system behaviour in the context of autonomous systems by performing logic-based stream reasoning with the help of Semantic Web technologies, including ontologies and semantic subscriptions.
• Ying Li is a PhD student at the Database and Web Information Systems Group at IDA. Her research work focuses on debugging and completing ontologies.